Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition

Area of Science:

• Plant molecular biology
• Genomics
• Stress response in plants

Background:

• Plants reprogram gene expression to combat abiotic and biotic stresses.
• Synonymous codon usage frequency varies among genes, leading to codon usage bias.

Purpose of the Study:

• Investigate the correlation between codon usage bias, gene expression, and underlying mechanisms in rice under stress.
• Identify target codons for developing climate-resilient rice varieties.

Main Methods:

• Analysis of gene expression (up- or downregulated) in rice under stress conditions.
• Assessment of codon usage bias, GC content, and effective number of codons.
• Evaluation of mutational pressure and natural selection pressure on gene expression.

Main Results:

• Highly expressed genes (up- or downregulated) exhibit high GC content (≥60%) and strong bias towards C/G at the third codon position.
• TTC, ATC, and CTC were most preferred codons; TAC, CAC, AAC, GAC, and TGC were moderately preferred.
• Downregulated genes are influenced by mutational pressure (R² ≥ 0.5), while upregulated genes are under natural selection pressure (R² ≤ 0.5).

Conclusions:

• Rice exhibits codon usage bias under stress, correlated with GC content, gene expression level, and gene length.
• Findings provide insights into optimizing gene codons for enhanced stress tolerance in rice.
• Identified codon preferences can guide the genetic engineering of climate-resilient rice varieties.